The Ofunato Bay in Iwate Prefecture, Japan, is an enclosed one located at the center of the Sanriku Rias coast in the northwestern region of the Pacific Ocean off Japan and providing an economically and environmentally important asset. To reveal the temporal and spatial changes of the microbial communities in this bay, the seawater samples were monthly collected in 2018 from 3 stations along its length covering the entire region each at upper (1 m) and deeper (8 or 10 m) depths. We sequenced cells trapped on 0.2-µm filters, targeting the free-living microbes only, among the sequentially size-fractionated samples on 20.0- 5.0- 0.8- and 0.2-µm filters. The whole genome shotgun sequencing was carried out with an Illumina MiSeq sequencing system.